Ion beam irradiation is a versatile tool for structural modification and engineering of new materials. In this study, 12‐tungstophosphoric acid (WPA) films of different thickness were spin‐coated on platinized silicon substrate and irradiated with low energy hydrogen ions (10 keV) and swift heavy ions (Bi, Xe, and V) with energies up to 710 MeV. The different energy/fluence combinations allowed controllable structural changes that were investigated in detail using Raman and Infrared spectroscopy. For 120‐nm‐thick WPA samples, the irradiation led to the decrease of intensity of the skeletal and W‐Oc‐W bands of Keggin anion in order: Bi < V < Xe (for their applied energy/fluence combination). Also, symmetry change of Keggin anion similar to the one observed in the case of Keggin anions interacting with the supports was observed. For the selected ion beam irradiation parameters, xenon ion beam induced transformation of WPA to polytungstate. For 20‐μm‐thick WPA samples, the irradiation with hydrogen ion beam induced changes of skeletal vibrations and increased individualistic behavior of Keggin anions. As the fluence increased, the amount of the Keggin anions partially transformed to bronze also increased. Irradiation with vanadium also caused transformation to bronze‐like structure but with higher ratio of terminal W=Od bonds. The overall results show clear correlation between degree of structural modification of WPA and the calculated displacement per atom value. These results open possibilities for engineering new catalytically active structures of polyoxometalates with the help of ion beams. In this study, 12‐tungstophosphoric acid (WPA) films (120 nm and 20 μm) were irradiated with hydrogen (10 keV) and swift heavy ions (Bi, Xe, and V, up to 710 MeV). The different energy/fluence combinations allowed controllable changes, from breaking of symmetry to bronze‐like structures, that were investigated in detail using Raman and Infrared spectroscopy. Structural changes of ion beam irradiated WPA might be beneficial for application in catalysis where the engineered structures can produce additional active sites for different reactions.